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Hasan M, Nishat ZS, Hasan MS, Hossain T, Ghosh A. Identification of m 6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli. Biochem Biophys Rep 2024; 38:101677. [PMID: 38511186 PMCID: PMC10950732 DOI: 10.1016/j.bbrep.2024.101677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.
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Affiliation(s)
| | | | - Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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Zhang J, Yao S, Cheng X, Zhao Y, Yu W, Ren X, Ji K, Yu Q. Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora. Int J Mol Sci 2024; 25:5960. [PMID: 38892149 PMCID: PMC11173211 DOI: 10.3390/ijms25115960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid-liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees.
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Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yulu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenya Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xingyue Ren
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
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Cheng X, Yao S, Zhang J, Wang D, Xu S, Yu Q, Ji K. Genome-Wide Identification and Expression Analysis of YTH Gene Family for Abiotic Stress Regulation in Camellia chekiangoleosa. Int J Mol Sci 2024; 25:3996. [PMID: 38612806 PMCID: PMC11012946 DOI: 10.3390/ijms25073996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
N6-methyladenosine (m6A) is essential for RNA metabolism in cells. The YTH domain, conserved in the kingdom of Eukaryotes, acts as an m6A reader that binds m6A-containing RNA. In plants, the YTH domain is involved in plant hormone signaling, stress response regulation, RNA stability, translation, and differentiation. However, little is known about the YTH genes in tea-oil tree, which can produce edible oil with high nutritional value. This study aims to identify and characterize the YTH domains within the tea-oil tree (Camellia chekiangoleosa Hu) genome to predict their potential role in development and stress regulation. In this study, 10 members of the YTH family containing the YTH domain named CchYTH1-10 were identified from C. chekiangoleosa. Through analysis of their physical and chemical properties and prediction of subcellular localization, it is known that most family members are located in the nucleus and may have liquid-liquid phase separation. Analysis of cis-acting elements in the CchYTH promoter region revealed that these genes could be closely related to abiotic stress and hormones. The results of expression profiling show that the CchYTH genes were differentially expressed in different tissues, and their expression levels change under drought stress. Overall, these findings could provide a foundation for future research regarding CchYTHs in C. chekiangoleosa and enrich the world in terms of epigenetic mark m6A in forest trees.
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Affiliation(s)
- Xiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jingjing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dengbao Wang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Shaojun Xu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (S.Y.); (J.Z.); (D.W.); (S.X.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Su H, Meng L, Qu Z, Zhang W, Liu N, Cao P, Jin J. Genome-wide identification of the N 6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.). BMC PLANT BIOLOGY 2024; 24:134. [PMID: 38403644 PMCID: PMC10895791 DOI: 10.1186/s12870-024-04813-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/09/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) is one of the common internal RNA modifications found in eukaryotes. The m6A modification can regulate various biological processes in organisms through the modulation of alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay of multiple types of RNA, without altering the nucleotide sequence. The three components involved in m6A modification, namely writer, eraser, and reader, mediate the abundance of RNA m6A modification through complex collaborative actions. Currently, research on m6A regulatory genes in plants is still in its infancy. RESULTS In this study, we identified 52 candidate m6A regulatory genes in common tobacco (Nicotiana tabacum L.). Gene structure, conserved domains, and motif analysis showed structural and functional diversity among different subgroups of tobacco m6A regulatory genes. The amplification of m6A regulatory genes were mainly driven by polyploidization and dispersed duplication, and duplicated genes evolved through purified selection. Based on the potential regulatory network and expression pattern analysis of m6A regulatory genes, a significant number of m6A regulatory genes might play important roles in growth, development, and stress response processes. Furthermore, we have confirmed the critical role of NtFIP37B, an m6A writer gene in tobacco, in enhancing drought resistance. CONCLUSIONS This study provides useful information for better understanding the evolution of m6A regulatory genes and the role of m6A modification in tobacco stress response, and lays the foundation for further elucidating the function of m6A regulatory genes in tobacco.
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Affiliation(s)
- Huan Su
- Beijing Life Science Academy, Beijing, 102200, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Lijun Meng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zechao Qu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Wei Zhang
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Nan Liu
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Peijian Cao
- Beijing Life Science Academy, Beijing, 102200, China.
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
| | - Jingjing Jin
- Beijing Life Science Academy, Beijing, 102200, China.
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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Fan S, Xu X, Chen J, Yin Y, Zhao Y. Genome-wide identification, characterization, and expression analysis of m6A readers-YTH domain-containing genes in alfalfa. BMC Genomics 2024; 25:18. [PMID: 38166738 PMCID: PMC10759653 DOI: 10.1186/s12864-023-09926-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) are often modified with methyl groups at the N6 position of adenosine (m6A), and these changes are interpreted by YTH domain-containing proteins to regulate the metabolism of m6A-modified mRNAs. Although alfalfa (Medicago sativa) is an established model organism for forage development, the understanding of YTH proteins in alfalfa is still limited. In the present investigation, 53 putative YTH genes, each encoding a YT521 domain-containing protein, were identified within the alfalfa genome. These genes were categorized into two subfamilies: YTHDF (49 members) and YTHDC (four members). Each subfamily demonstrates analogous motif distributions and domain architectures. Specifically, proteins encoded by MsYTHDF genes incorporate a single domain structure, while those corresponding to MsYTH5, 8, 12, 16 who are identified as members of the MsYTHDC subfamily, exhibit CCCH-type zinc finger repeats at their N-termini. It is also observed that the predicted aromatic cage pocket that binds the m6A residue of MsYTHDC consists of a sequence of two tryptophan residues and one tyrosine residue (WWY). Conversely, in MsYTHDF, the binding pocket comprises two highly conserved tryptophan residues and either one tryptophan residue (WWW) or tyrosine residue (WWY) in MsYTHDF.Through comparative analysis of qRT-PCR data, we observed distinct expression patterns in specific genes under abiotic stress, indicating their potential regulatory roles. Notably, five genes (MsYTH2, 14, 26, 27, 48) consistently exhibit upregulation, and two genes (MsYTH33, 35) are downregulated in response to both cold and salt stress. This suggests a common mechanism among these YTH proteins in response to various abiotic stressors in alfalfa. Further, integrating qRT-PCR with RNA-seq data revealed that MsYTH2, MsYTH14, and MsYTH16 are highly expressed in leaves at various development stages, underscoring their potential roles in regulating the growth of these plant parts. The obtained findings shed further light on the biological functions of MsYTH genes and may aid in the selection of suitable candidate genes for future genetic enhancement endeavors aimed at improving salt and cold tolerance in alfalfa.
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Affiliation(s)
- Shugao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Xiao Xu
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Jianmin Chen
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yanling Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai, China.
| | - Ying Zhao
- School of Resources and Environmental Engineering, Ludong University, Yantai, China.
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Seigneurin-Berny D, Karczewski C, Delaforge E, Yaacoub K, Gaspar Litholdo C, Favory JJ, Ringkjøbing Jensen M, Bousquet-Antonelli C, Verdel A. ECT2 peptide sequences outside the YTH domain regulate its m 6A-RNA binding. RNA Biol 2024; 21:1-13. [PMID: 39267376 PMCID: PMC11404569 DOI: 10.1080/15476286.2024.2399914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/16/2024] [Accepted: 08/28/2024] [Indexed: 09/17/2024] Open
Abstract
The m6A epitranscriptomic mark is the most abundant and widespread internal RNA chemical modification, which through the control of RNA acts as an important factor of eukaryote reproduction, growth, morphogenesis and stress response. The main m6A readers constitute a super family of proteins with hundreds of members that share a so-called YTH RNA binding domain. The majority of YTH proteins carry no obvious additional domain except for an Intrinsically Disordered Region (IDR). In Arabidopsis thaliana IDRs are important for the functional specialization among the different YTH proteins, known as Evolutionarily Conserved C-Terminal region, ECT 1 to 12. Here by studying the ECT2 protein and using an in vitro biochemical characterization, we show that full-length ECT2 and its YTH domain alone have a distinct ability to bind m6A, conversely to previously characterized YTH readers. We identify peptide regions outside of ECT2 YTH domain, in the N-terminal IDR, that regulate its binding to m6A-methylated RNA. Furthermore, we show that the selectivity of ECT2 binding for m6A is enhanced by a high uridine content within its neighbouring sequence, where ECT2 N-terminal IDR is believed to contact the target RNA in vivo. Finally, we also identify small structural elements, located next to ECT2 YTH domain and conserved in a large set of YTH proteins, that enhance its binding to m6A-methylated RNA. We propose from these findings that some of these regulatory regions are not limited to ECT2 or YTH readers of flowering plants but may be widespread among eukaryotic YTH readers.
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Affiliation(s)
- Daphné Seigneurin-Berny
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences, Grenoble, France
| | - Claire Karczewski
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences, Grenoble, France
| | - Elise Delaforge
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Karen Yaacoub
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences, Grenoble, France
| | - Celso Gaspar Litholdo
- CNRS-LGDP-UMR5096, Université de Perpignan, Perpignan, France
- Université de Perpignan Via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS-LGDP-UMR5096, Université de Perpignan, Perpignan, France
- Université de Perpignan Via Domitia, Perpignan, France
| | | | - Cécile Bousquet-Antonelli
- CNRS-LGDP-UMR5096, Université de Perpignan, Perpignan, France
- Université de Perpignan Via Domitia, Perpignan, France
| | - André Verdel
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences, Grenoble, France
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Vicente AM, Manavski N, Rohn PT, Schmid LM, Garcia-Molina A, Leister D, Seydel C, Bellin L, Möhlmann T, Ammann G, Kaiser S, Meurer J. The plant cytosolic m 6A RNA methylome stabilizes photosynthesis in the cold. PLANT COMMUNICATIONS 2023; 4:100634. [PMID: 37287225 PMCID: PMC10721483 DOI: 10.1016/j.xplc.2023.100634] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/10/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
The sessile lifestyle of plants requires an immediate response to environmental stressors that affect photosynthesis, growth, and crop yield. Here, we showed that three abiotic perturbations-heat, cold, and high light-triggered considerable changes in the expression signatures of 42 epitranscriptomic factors (writers, erasers, and readers) with putative chloroplast-associated functions that formed clusters of commonly expressed genes in Arabidopsis. The expression changes under all conditions were reversible upon deacclimation, identifying epitranscriptomic players as modulators in acclimation processes. Chloroplast dysfunctions, particularly those induced by the oxidative stress-inducing norflurazon in a largely GENOME UNCOUPLED-independent manner, triggered retrograde signals to remodel chloroplast-associated epitranscriptomic expression patterns. N6-methyladenosine (m6A) is known as the most prevalent RNA modification and impacts numerous developmental and physiological functions in living organisms. During cold treatment, expression of components of the primary nuclear m6A methyltransferase complex was upregulated, accompanied by a significant increase in cellular m6A mRNA marks. In the cold, the presence of FIP37, a core component of the writer complex, played an important role in positive regulation of thylakoid structure, photosynthetic functions, and accumulation of photosystem I, the Cytb6f complex, cyclic electron transport proteins, and Curvature Thylakoid1 but not that of photosystem II components and the chloroplast ATP synthase. Downregulation of FIP37 affected abundance, polysomal loading, and translation of cytosolic transcripts related to photosynthesis in the cold, suggesting m6A-dependent translational regulation of chloroplast functions. In summary, we identified multifaceted roles of the cellular m6A RNA methylome in coping with cold; these were predominantly associated with chloroplasts and served to stabilize photosynthesis.
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Affiliation(s)
- Alexandre Magno Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Paul Torben Rohn
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Antoni Garcia-Molina
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Charlotte Seydel
- Plant Development, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Leo Bellin
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Erwin-Schrödinger-Street, 7, 67663 Kaiserslautern, Germany
| | - Torsten Möhlmann
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Erwin-Schrödinger-Street, 7, 67663 Kaiserslautern, Germany
| | - Gregor Ammann
- Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Stefanie Kaiser
- Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany.
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Dhingra Y, Gupta S, Gupta V, Agarwal M, Katiyar-Agarwal S. The emerging role of epitranscriptome in shaping stress responses in plants. PLANT CELL REPORTS 2023; 42:1531-1555. [PMID: 37481775 DOI: 10.1007/s00299-023-03046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
KEY MESSAGE RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.
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Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007, India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Ramappa S, Joshi MA, Krishna H, Dunna V, Jain N, Sreevathsa R, Devate NB. Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study. Genes (Basel) 2023; 14:1902. [PMID: 37895250 PMCID: PMC10606372 DOI: 10.3390/genes14101902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat's capacity to withstand moisture deficit stress during seed germination and early growth stages is fundamental in improving its overall performance. However, the genetic regulation of moisture deficit stress tolerance during the seed germination phase remains largely unexplored. In this study, a total of 193 wheat genotypes were subjected to simulated moisture deficit stress using PEG-6000 (-0.4 MPa) during the seed germination stage. The induced moisture deficit stress significantly reduced various seedling-vigour-related traits. The genetic regions linked to these traits were found using a genome-wide association study (GWAS). The analysis identified 235 MTAs with a significance -log10(p) value of >4. After applying the Bonferroni correction, the study identified 47 unique single nucleotide polymorphisms (SNPs) that are linked to candidate genes important for the trait of interest. The current study emphasises the effectiveness of genome-wide association studies (GWAS) in identifying promising candidate genes, improving wheat seedling vigour and root traits, and offering essential information for the development of wheat cultivars tolerant to moisture deficit stress.
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Affiliation(s)
- S Ramappa
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Monika A. Joshi
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vijay Dunna
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rohini Sreevathsa
- Division of Molecular Biology and Biotechnology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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10
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Han Z, Yi X, Li J, Zhang T, Liao D, You J, Ai J. RNA m 6A modification in prostate cancer: A new weapon for its diagnosis and therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188961. [PMID: 37507057 DOI: 10.1016/j.bbcan.2023.188961] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/21/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023]
Abstract
Prostate cancer (PCa) is the most common malignant tumor and the second leading cause of cancer-related mortality in men worldwide. Despite significant advances in PCa therapy, the underlying molecular mechanisms have yet to be fully elucidated. Recently, epigenetic modification has emerged as a key player in tumor progression, and RNA-based N6-methyladenosine (m6A) epigenetic modification was found to be crucial. This review summarizes comprehensive state-of-art mechanisms underlying m6A modification, its implication in the pathogenesis, and advancement of PCa in protein-coding and non-coding RNA contexts, its relevance to PCa immunotherapy, and the ongoing clinical trials for PCa treatment. This review presents potential m6A-based targets and paves a new avenue for diagnosing and treating PCa, providing new guidelines for future related research through a systematic review of previous results.
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Affiliation(s)
- Zeyu Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China
| | - Xianyanling Yi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China
| | - Jin Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China
| | - Tianyi Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China
| | - Dazhou Liao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China
| | - Jia You
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China
| | - Jianzhong Ai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, 88 South Keyuan Road, Chengdu 610041, China.
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Lin H, Shi T, Zhang Y, He C, Zhang Q, Mo Z, Pan W, Nie X. Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii. PLANTS (BASEL, SWITZERLAND) 2023; 12:2747. [PMID: 37514361 PMCID: PMC10385245 DOI: 10.3390/plants12142747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops.
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Affiliation(s)
- Huiyuan Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Tingrui Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Ying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Chuyang He
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Qiying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Zhiping Mo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
- Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Yangling 712100, China
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12
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Li B, Zhang M, Sun W, Yue D, Ma Y, Zhang B, Duan L, Wang M, Lindsey K, Nie X, Zhang X, Yang X. N6-methyladenosine RNA modification regulates cotton drought response in a Ca 2+ and ABA-dependent manner. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1270-1285. [PMID: 36949572 DOI: 10.1111/pbi.14036] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 05/27/2023]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post-transcriptional levels. However, the biological function and regulatory mechanism of m6 A modification in the drought stress response is still poorly understood. We generated a transcriptome-wide m6 A map using drought-resistant and drought-sensitive varieties of cotton under different water deficient conditions to uncover patterns of m6 A methylation in cotton response to drought stress. The results reveal that m6 A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m6 A was deposited in the drought-resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m6 A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m6 A levels, facilitating the mRNA decay of ABA signal-related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca2+ signal-related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus-induced gene silencing (VIGS) of two Ca2+ -related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m6 A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post-transcriptional modification involved in affecting drought response in cotton, by mediating m6 A methylation on targeted transcripts in the ABA and Ca2+ signalling transduction pathways.
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Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mengmeng Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Boyang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingfeng Duan
- College of Engineering, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Xinjiang, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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13
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Xu P, Li X, Fan J, Wang C, Lin A, Lian H. Comprehensive Identification and Expression Analysis of the YTH Family of RNA-Binding Proteins in Strawberry. PLANTS (BASEL, SWITZERLAND) 2023; 12:1449. [PMID: 37050075 PMCID: PMC10097400 DOI: 10.3390/plants12071449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Plant growth and development processes are tightly regulated at multiple levels, including transcriptional and post-transcriptional levels, and the RNA-binding protein YTH regulates gene expression during growth and development at the post-transcriptional level by regulating RNA splicing, processing, stability, and translation. We performed a systematic characterization of YTH genes in diploid forest strawberry and identified a total of nine YTH genes. With the help of phylogenetic analysis, these nine genes were found to belong to two different groups, YTHDC and YTHDF, with YTHDF being further subdivided into three subfamilies. Replication analysis showed that YTH3 and YTH4 are a gene pair generated by tandem repeat replication. These two genes have similarities in gene structure, number of motifs, and distribution patterns. Promoter analysis revealed the presence of multiple developmental, stress response, and hormone-response-related cis-elements. Analysis of available transcriptome data showed that the expression levels of most of the YTH genes were stable with no dramatic changes during development in different tissues. However, YTH3 maintained high expression levels in all tissues and during fruit development, and YTH4 was expressed at higher levels in tissues such as flowers, leaves, and seedlings, while it was significantly lower than YTH3 in white fruits and ripening fruits with little fluctuation. Taken together, our study provides insightful and comprehensive basic information for the study of YTH genes in strawberry.
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14
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Hao W, Wang W, Xiao X, Sun J, Wu B, Zhao Y, Pei S, Fan W, Xu D, Qin T. Genome-Wide Identification and Evolutionary Analysis of Gossypium YTH Domain-Containing RNA-Binding Protein Family and the Role of GhYTH8 in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:1198. [PMID: 36904058 PMCID: PMC10006896 DOI: 10.3390/plants12051198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
YTH domain-containing proteins are one kind of RNA-binding protein involved in post-transcriptional regulation and play multiple roles in regulating the growth, development, and abiotic stress responses of plants. However, the YTH domain-containing RNA-binding protein family has not been previously studied in cotton. In this study, a total of 10, 11, 22, and 21 YTH genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium barbadense, and Gossypium hirsutum, respectively. These Gossypium YTH genes were categorized into three subgroups by phylogenetic analysis. The chromosomal distribution, synteny analysis, structures of Gossypium YTH genes, and the motifs of YTH proteins were analyzed. Furthermore, the cis-element of GhYTH genes promoter, miRNA targets of GhYTH genes, and subcellular localization of GhYTH8 and GhYTH16 were characterized. Expression patterns of GhYTH genes in different tissues, organs, and in response to different stresses were also analyzed. Moreover, functional verifications revealed that silencing GhYTH8 attenuated the drought tolerance in the upland cotton TM-1 line. These findings provide useful clues for the functional and evolutionary analysis of YTH genes in cotton.
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Affiliation(s)
- Wei Hao
- College of Medical Technology, Beihua University, Jilin City 132013, China
| | - Weipeng Wang
- College of Agriculture, Liaocheng University, Liaocheng 252000, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 410700, China
| | - Xiangfen Xiao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jialiang Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 410700, China
| | - Bingjie Wu
- College of Agriculture, Liaocheng University, Liaocheng 252000, China
| | - Yuping Zhao
- College of Agriculture, Liaocheng University, Liaocheng 252000, China
| | - Shuaishuai Pei
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 410700, China
| | - Wenjia Fan
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 410700, China
| | - Dongbei Xu
- College of Agronomy, Sichuan Agricultural University, Chengdu 625014, China
| | - Tengfei Qin
- College of Agriculture, Liaocheng University, Liaocheng 252000, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 410700, China
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15
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Zhang H, Yuan Y, Xing H, Xin M, Saeed M, Wu Q, Wu J, Zhuang T, Zhang X, Mao L, Sun X, Song X, Wang Z. Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1139526. [PMID: 36950351 PMCID: PMC10025482 DOI: 10.3389/fpls.2023.1139526] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The HVA22 family of genes, induced by abscisic acid and stress, encodes a class of stress response proteins with a conserved TB2/DP1/HVA22 domain that are unique among eukaryotes. Previous studies have shown that HVA22s play an important role in plant responses to abiotic stresses. In the present study, 34, 32, 16, and 17 HVA22s were identified in G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively. These HVA22 genes were classified into nine subgroups, randomly distributed on the chromosomes. Synteny analysis showed that the amplification of the HVA22s were mainly due to segmental duplication or whole genome replication (WGD). Most HVA22s promoter sequences contain a large number of drought response elements (MYB), defense and stress response elements (TC-rich repeats), and hormone response elements (ABRE, ERE, SARE, etc.), suggesting that HVA22s may respond to adversity stresses. Expression profiling demonstrated that most GhHVA22s showed a constitutive expression pattern in G. hirsutum and could respond to abiotic stresses such as salt, drought, and low temperature. Overexpression of GhHVA22E1D (GH_D07G0564) in Arabidopsis thaliana enhances salt and drought tolerance in Arabidopsis. Virus-induced gene silencing of GhHVA22E1D reduced salt and drought tolerance in cotton. This indicates that GhHVA22E1D plays an active role in the plant response to salt stress and drought stress. GhHVA22E1D may act in plant response to adversity by altering the antioxidant capacity of plants. This study provides valuable information for the functional genomic study of the HVA22 gene family in cotton. It also provides a reference for further elucidation of the functional studies of HVA22 in plant resistance to abiotic stress response.
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Affiliation(s)
- Haijun Zhang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Yanchao Yuan
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
- College of Life Sciences, Qingdao Agricultural University, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao, China
| | - Huixian Xing
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Ming Xin
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Muhammad Saeed
- Department of Agricultural Sciences, College of Agriculture and Environmental Sciences, Faculty of Life Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qi Wu
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Jing Wu
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Tao Zhuang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Lili Mao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Xuezhen Sun
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Xianliang Song
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Zongwen Wang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
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16
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Wang S, Li H, Lian Z, Deng S. The Role of m 6A Modifications in B-Cell Development and B-Cell-Related Diseases. Int J Mol Sci 2023; 24:4721. [PMID: 36902149 PMCID: PMC10003095 DOI: 10.3390/ijms24054721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
B cells are a class of professional antigen-presenting cells that produce antibodies to mediate humoral immune response and participate in immune regulation. m6A modification is the most common RNA modification in mRNA; it involves almost all aspects of RNA metabolism and can affect RNA splicing, translation, stability, etc. This review focuses on the B-cell maturation process as well as the role of three m6A modification-related regulators-writer, eraser, and reader-in B-cell development and B-cell-related diseases. The identification of genes and modifiers that contribute to immune deficiency may shed light on regulatory requirements for normal B-cell development and the underlying mechanism of some common diseases.
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Affiliation(s)
- Shuqi Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huanxiang Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
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Sun J, Bie XM, Chu XL, Wang N, Zhang XS, Gao XQ. Genome-edited TaTFL1-5 mutation decreases tiller and spikelet numbers in common wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1142779. [PMID: 36895877 PMCID: PMC9989183 DOI: 10.3389/fpls.2023.1142779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Tillering is a critical agronomic trait of wheat (Triticum aestivum L.) that determines the shoot architecture and affects grain yield. TERMINAL FLOWER 1 (TFL1), encoding a phosphatidylethanolamine-binding protein, is implicated in the transition to flowering and shoot architecture in plant development. However, the roles of TFL1 homologs is little known in wheat development. CRISPR/Cas9-mediated targeted mutagenesis was used in this study to generate a set of wheat (Fielder) mutants with single, double or triple-null tatfl1-5 alleles. The wheat tatfl1-5 mutations decreased the tiller number per plant in the vegetative growth stage and the effective tiller number per plant and spikelet number per spike at maturity in the field. RNA-seq analysis showed that the expression of the auxin signaling-related and cytokinin signaling-related genes was significantly changed in the axillary buds of tatfl1-5 mutant seedlings. The results suggested that wheat TaTFL1-5s were implicated in tiller regulation by auxin and cytokinin signaling.
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18
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Mulozi L, Vennapusa AR, Elavarthi S, Jacobs OE, Kulkarni KP, Natarajan P, Reddy UK, Melmaiee K. Transcriptome profiling, physiological, and biochemical analyses provide new insights towards drought stress response in sugar maple ( Acer saccharum Marshall) saplings. FRONTIERS IN PLANT SCIENCE 2023; 14:1150204. [PMID: 37152134 PMCID: PMC10154611 DOI: 10.3389/fpls.2023.1150204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
Sugar maple (Acer saccharum Marshall) is a temperate tree species in the northeastern parts of the United States and is economically important for its hardwood and syrup production. Sugar maple trees are highly vulnerable to changing climatic conditions, especially drought, so understanding the physiological, biochemical, and molecular responses is critical. The sugar maple saplings were subjected to drought stress for 7, 14, and 21 days and physiological data collected at 7, 14, and 21 days after stress (DAS) showed significantly reduced chlorophyll and Normalized Difference Vegetation Index with increasing drought stress time. The drought stress-induced biochemical changes revealed a higher accumulation of malondialdehyde, proline, and peroxidase activity in response to drought stress. Transcriptome analysis identified a total of 14,099 differentially expressed genes (DEGs); 328 were common among all stress periods. Among the DEGs, transcription factors (including NAC, HSF, ZFPs, GRFs, and ERF), chloroplast-related and stress-responsive genes such as peroxidases, membrane transporters, kinases, and protein detoxifiers were predominant. GO enrichment and KEGG pathway analysis revealed significantly enriched processes related to protein phosphorylation, transmembrane transport, nucleic acids, and metabolic, secondary metabolite biosynthesis pathways, circadian rhythm-plant, and carotenoid biosynthesis in response to drought stress. Time-series transcriptomic analysis revealed changes in gene regulation patterns in eight different clusters, and pathway analysis by individual clusters revealed a hub of stress-responsive pathways. In addition, qRT-PCR validation of selected DEGs revealed that the expression patterns were consistent with transcriptome analysis. The results from this study provide insights into the dynamics of physiological, biochemical, and gene responses to progressive drought stress and reveal the important stress-adaptive mechanisms of sugar maple saplings in response to drought stress.
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Affiliation(s)
- Lungowe Mulozi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Amaranatha R. Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Sathya Elavarthi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
- *Correspondence: Kalpalatha Melmaiee, ; Sathya Elavarthi,
| | - Oluwatomi E. Jacobs
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Krishnanand P. Kulkarni
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Purushothaman Natarajan
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Umesh K. Reddy
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
- *Correspondence: Kalpalatha Melmaiee, ; Sathya Elavarthi,
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19
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Hu J, Cai J, Xu T, Kang H. Epitranscriptomic mRNA modifications governing plant stress responses: underlying mechanism and potential application. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2245-2257. [PMID: 36002976 PMCID: PMC9674322 DOI: 10.1111/pbi.13913] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 06/01/2023]
Abstract
Plants inevitably encounter environmental adversities, including abiotic and biotic stresses, which significantly impede plant growth and reduce crop yield. Thus, fine-tuning the fate and function of stress-responsive RNAs is indispensable for plant survival under such adverse conditions. Recently, post-transcriptional RNA modifications have been studied as a potent route to regulate plant gene expression under stress. Among over 160 mRNA modifications identified to date, N6 -methyladenosine (m6 A) in mRNAs is notable because of its multifaceted roles in plant development and stress response. Recent transcriptome-wide mapping has revealed the distribution and patterns of m6 A in diverse stress-responsive mRNAs in plants, building a foundation for elucidating the molecular link between m6 A and stress response. Moreover, the identification and characterization of m6 A writers, readers and erasers in Arabidopsis and other model crops have offered insights into the biological roles of m6 A in plant abiotic stress responses. Here, we review the recent progress of research on mRNA modifications, particularly m6 A, and their dynamics, distribution, regulation and biological functions in plant stress responses. Further, we posit potential strategies for breeding stress-tolerant crops by engineering mRNA modifications and propose the future direction of research on RNA modifications to gain a much deeper understanding of plant stress biology.
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Affiliation(s)
- Jianzhong Hu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
| | - Hunseung Kang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
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20
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Zhou L, Gao G, Tang R, Wang W, Wang Y, Tian S, Qin G. m 6 A-mediated regulation of crop development and stress responses. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1447-1455. [PMID: 35178842 PMCID: PMC9342612 DOI: 10.1111/pbi.13792] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 05/12/2023]
Abstract
Dynamic chemical modifications in eukaryotic messenger RNAs (mRNAs) constitute an essential layer of gene regulation, among which N6 -methyladenosine (m6 A) was unveiled to be the most abundant. m6 A functionally modulates important biological processes in various mammals and plants through the regulation of mRNA metabolism, mainly mRNA degradation and translation efficiency. Physiological functions of m6 A methylation are diversified and affected by intricate sequence contexts and m6 A machineries. A number of studies have dissected the functional roles and the underlying mechanisms of m6 A modifications in regulating plant development and stress responses. Recently, it was demonstrated that the human FTO-mediated plant m6 A removal caused dramatic yield increases in rice and potato, indicating that modulation of m6 A methylation could be an efficient strategy for crop improvement. In this review, we summarize the current progress concerning the m6 A-mediated regulation of crop development and stress responses, and provide an outlook on the potential application of m6 A epitranscriptome in the future improvement of crops.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guangtong Gao
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Renkun Tang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weihao Wang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuying Wang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shiping Tian
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guozheng Qin
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
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21
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Zhai G, Xiao L, Jiang C, Yue S, Zhang M, zheng J, Liu Z, Dong Y. Regulatory Role of N6-Methyladenosine (m6A) Modification in Osteoarthritis. Front Cell Dev Biol 2022; 10:946219. [PMID: 35846376 PMCID: PMC9282717 DOI: 10.3389/fcell.2022.946219] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Osteoarthritis (OA) is the most common joint disease, usually occurring in middle-aged and elderly people. However, current treatment for OA in its early stages is ineffective, and drug therapy is often ineffective in slowing the progression of the disease. In fact, a deeper understanding of the underlying molecular mechanisms of OA could help us to better develop effective therapeutic measures. N6-methyladenosine (m6A) is a methylation that occurs at the adenosine N6-position, which is the most common internal modification on eukaryotic mRNAs. The role and mechanisms of m6A in mammalian gene regulation have been extensively studied. The “Writer”, “eraser”, and “reader” proteins are key proteins involved in the dynamic regulation of m6A modifications. Recent studies on post-transcriptional regulation alone have shown that m6a modification has an important role in the development of OA. This paper summarizes the specific regulatory processes of M6A in disease and reviews the role of m6A in OA, describing its pathophysiological role and molecular mechanisms, as well as its future research trends and potential clinical applications in OA.
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Affiliation(s)
- Ganggang Zhai
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Likang Xiao
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Chenyang Jiang
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Songkai Yue
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Meng Zhang
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Jia zheng
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Zeming Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yonghui Dong, ; Zeming Liu,
| | - Yonghui Dong
- Department of Orthopedics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
- Microbiome Laboratory, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yonghui Dong, ; Zeming Liu,
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22
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Genome-Wide Identification, Classification and Expression Analysis of m 6A Gene Family in Solanum lycopersicum. Int J Mol Sci 2022; 23:ijms23094522. [PMID: 35562913 PMCID: PMC9100520 DOI: 10.3390/ijms23094522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Advanced knowledge of messenger RNA (mRNA) N6-methyladenosine (m6A) and DNA N6-methyldeoxyadenosine (6 mA) redefine our understanding of these epigenetic modifications. Both m6A and 6mA carry important information for gene regulation, and the corresponding catalytic enzymes sometimes belong to the same gene family and need to be distinguished. However, a comprehensive analysis of the m6A gene family in tomato remains obscure. Here, 24 putative m6A genes and their family genes in tomato were identified and renamed according to BLASTP and phylogenetic analysis. Chromosomal location, synteny, phylogenetic, and structural analyses were performed, unravelling distinct evolutionary relationships between the MT-A70, ALKBH, and YTH protein families, respectively. Most of the 24 genes had extensive tissue expression, and 9 genes could be clustered in a similar expression trend. Besides, SlYTH1 and SlYTH3A showed a different expression pattern in leaf and fruit development. Additionally, qPCR data revealed the expression variation under multiple abiotic stresses, and LC-MS/MS determination exhibited that the cold stress decreased the level of N6 2′-O dimethyladenosine (m6Am). Notably, the orthologs of newly identified single-strand DNA (ssDNA) 6mA writer–eraser–reader also existed in the tomato genome. Our study provides comprehensive information on m6A components and their family proteins in tomato and will facilitate further functional analysis of the tomato N6-methyladenosine modification genes.
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23
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Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
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Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
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24
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Zhang Y, Zhang S, Shi M, Li M, Zeng J, He J. Roles of m6A modification in neurological diseases. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2022; 47:109-115. [PMID: 35545370 PMCID: PMC10930482 DOI: 10.11817/j.issn.1672-7347.2022.200990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A) methylation modification is one of the most common epigenetic modifications for eukaryotic mRNA. Under the catalytic regulation of relevant enzymes, m6A participates in the body's pathophysiological processes via mediating RNA transcription, splicing, translation, and decay. In the past, we mainly focused on the regulation of m6A in tumors such as hematological tumors, cervical cancer, breast cancer. In recent years, it has been found that m6A is enriched in mRNAs of neurogenesis, cell cycle, and neuron differentiation. Its regulation in the nervous system is gradually being recognized. When the level of m6A modification and the expression levels of relevant enzyme proteins are changed, it will cause neurological dysfunction and participate in the occurrence and conversion of neurological diseases. Recent studies have found that the m6A modification and its associated enzymes were involved in major depressive disorder, Parkinson's disease, Alzheimer's disease, Fragile X syndrome, amyotrophic lateral sclerosis, and traumatic brain injury, and they also play a key role in the development of neurological diseases and many other neurological diseases. This paper mainly reviewed the recent progress of m6A modification-related enzymes, focusing on the impact of m6A modification and related enzyme-mediated regulation of gene expression on the central nervous system diseases, so as to provide potential targets for the prevention of neurological diseases.
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Affiliation(s)
- Yuan Zhang
- Cancer Research Institute, Key Laboratory of Cancer Cellular and Molecular Pathology of Hunan Province, Hengyang Medical College, University of South China, Hengyang Hunan 421001.
| | - Si Zhang
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang Hunan 421001
| | - Mengmeng Shi
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang Hunan 421001
| | - Menglin Li
- Department of Endocrinology, First Affiliated Hospital of University of South China, Hengyang Hunan 421001, 4. Department of Pathology, Hainan Medical College, Haikou 571199, China
| | - Jiayu Zeng
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang Hunan 421001
| | - Jie He
- Cancer Research Institute, Key Laboratory of Cancer Cellular and Molecular Pathology of Hunan Province, Hengyang Medical College, University of South China, Hengyang Hunan 421001.
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25
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Shao Y, Wong CE, Shen L, Yu H. N 6-methyladenosine modification underlies messenger RNA metabolism and plant development. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102047. [PMID: 33965696 DOI: 10.1016/j.pbi.2021.102047] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
RNA modifications constitute an essential layer of gene regulation in living organisms. As the most prevalent internal modification on eukaryotic mRNAs, N6-methyladenosine (m6A) exists in many plant species and requires the evolutionarily conserved methyltransferases, demethylases, and m6A binding proteins for writing, erasing, and reading m6A, respectively. In plants, m6A affects many aspects of mRNA metabolism, including alternative polyadenylation, secondary structure, translation, and decay, which underlies various plant developmental processes and stress responses. Here, we discuss the recent progress in understanding the roles of m6A modification in mRNA metabolism and their mechanistic link with plant development and stress responses. We also highlight some outstanding questions and provide an outlook on future prospects of m6A research in plants.
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Affiliation(s)
- Yanlin Shao
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
| | - Chui Eng Wong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore.
| | - Hao Yu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
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26
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Shao DJ, Wei YM, Yu ZQ, Dai X, Gao XQ. Arabidopsis AtPRP17 functions in embryo development by regulating embryonic patterning. PLANTA 2021; 254:58. [PMID: 34426887 DOI: 10.1007/s00425-021-03702-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Arabidopsis AtPRP17, a homolog of yeast splicing factor gene PRP17, is expressed in siliques and embryos and functions in embryo development via regulating embryonic patterning. Yeast splicing factor PRP17/CDC40 is essential for cell growth through involvement in cell cycle regulation. Arabidopsis genome encodes a homolog of PRP17, AtPRP17; however, its function in Arabidopsis development is unknown. This study showed that AtPRP17 was highly expressed in siliques and embryos, and the protein was localized in the nucleus. The loss-of-function mutation of AtPRP17 led to shrunken seeds in Arabidopsis mature siliques. Further analysis revealed that the defective mature seeds of the mutant resulted from abnormal embryos with shriveled cotyledons, unequal cotyledons, swollen and shortened hypocotyls, or shortened radicles. During embryogenesis, mutant embryos showed delayed development and defective patterning of the apical and base domains, such as inhibited cotyledons and disorganized quiescent center cells and columella. Our results suggested that AtPRP17 functions in Arabidopsis embryo development via regulating embryonic patterning.
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Affiliation(s)
- Dong Jie Shao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Yi Ming Wei
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Zhong Qing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin-Qi Gao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China.
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27
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Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview. Int J Mol Sci 2021; 22:ijms22136731. [PMID: 34201749 PMCID: PMC8269355 DOI: 10.3390/ijms22136731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.
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28
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Yu CY, Zhang HK, Wang N, Sun J, Dong YX, Zhang XS, Gao XQ. Characterization of the ERP gene family in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2021; 16:1913301. [PMID: 33906568 PMCID: PMC8143257 DOI: 10.1080/15592324.2021.1913301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
Plant genomes encode numerous proteins with obscure features (POFs) that lack recognized domains or motifs. However, there is little functional information for POFs even in Arabidopsis because biochemical, physiological, and genetic assay are required for the functional annotations of POFs. Here, we identified a small gene family, the endoplasmic reticulum-localized POF (ERP) family, in Arabidopsis. Phylogenetic analysis revealed that the number of ERP family members was conserved in the plant kingdom, suggesting strong selective pressure was imposed on ERP family during plant evolution. No recognizable domains were identified in the predicted ERP proteins, except for the N-terminal signal peptide. ERPs were found to be widely expressed during Arabidopsis development and showed endoplasmic reticulum localization. It was reported that ERP1 is an inositol-1,4,5-trisphosphate 5-phosphatase (5PTase), but ERP1 could not substitute for At5PTase12 in precocious pollen germination, indicating that ERP1 did not have the similar functions as At5PTase12 in inositol 1,4,5-trisphosphate [Ins(1,4,5)P3] metabolism. Further studies are needed to dissect the functions of ERP family proteins in Arabidopsis development.
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Affiliation(s)
- Cai Yu Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Huan Kai Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Ning Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Jing Sun
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Yu Xiu Dong
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Xian Sheng Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Xin-Qi Gao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
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29
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Shi R, Ying S, Li Y, Zhu L, Wang X, Jin H. Linking the YTH domain to cancer: the importance of YTH family proteins in epigenetics. Cell Death Dis 2021; 12:346. [PMID: 33795663 PMCID: PMC8016981 DOI: 10.1038/s41419-021-03625-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A), the most prevalent and reversible modification of mRNA in mammalian cells, has recently been extensively studied in epigenetic regulation. YTH family proteins, whose YTH domain can recognize and bind m6A-containing RNA, are the main "readers" of m6A modification. YTH family proteins perform different functions to determine the metabolic fate of m6A-modified RNA. The crystal structure of the YTH domain has been completely resolved, highlighting the important roles of several conserved residues of the YTH domain in the specific recognition of m6A-modified RNAs. Upstream and downstream targets have been successively revealed in different cancer types and the role of YTH family proteins has been emphasized in m6A research. This review describes the regulation of RNAs by YTH family proteins, the structural features of the YTH domain, and the connections of YTH family proteins with human cancers.
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Affiliation(s)
- Rongkai Shi
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Shilong Ying
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Yadan Li
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
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